Find vertices in .obj File which were marked in Blender
I imagine you've decided against separating those vertices so you only export each part separately, i.e. two individual obj files?

(Delete the section(s) you don't want to include in the first obj file, export what's left, then reload the Blender file, delete the other section and export that for the second obj file.

When both are imported their scaling and relative positions should still match so it's easy to recombine/join them (CTL-J) when imported back into Blender)